6U48

E. coli 50S with phazolicin (PHZ) bound in exit tunnel

This is a non-PDB format compatible entry.

Summary for 6U48

• Entry DOI: 10.2210/pdb6u48/pdb
• EMDB information: 20638
• Related PRD ID: PRD_002365
• Descriptor: 23S rRNA, 50S ribosomal protein uL13, 50S ribosomal protein uL14, ... (32 entities in total)
• Functional Keywords: ribosome, phazolicin, antimicrobial protein, ribosome-inhibitor complex, ribosome/inhibitor
• Biological source: Escherichia coli; More
• Total number of polymer chains: 32
• Total formula weight: 1352665.05

Authors

Watson, Z.L.,Cate, J.H.D.,Polikanov, Y.S.,Severinov, K. (deposition date: 2019-08-23, release date: 2019-09-18, Last modification date: 2023-11-15)

Primary citation

Travin, D.Y.,Watson, Z.L.,Metelev, M.,Ward, F.R.,Osterman, I.A.,Khven, I.M.,Khabibullina, N.F.,Serebryakova, M.,Mergaert, P.,Polikanov, Y.S.,Cate, J.H.D.,Severinov, K.
Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.
Nat Commun, 10:4563-4563, 2019

PubMed Abstract: Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) - an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.

PubMed: 31594941
DOI: 10.1038/s41467-019-12589-5

Experimental method

ELECTRON MICROSCOPY (2.87 Å)